Finding Fish and Frogs From a Water Sample: eDNA and Genetics at Mount Rainier

Until stocking began, all the lakes in Mount Rainier National Park had no fish at all. Between 1915 and 1972, over nine million fish were stocked into its lakes and streams, mostly to improve recreational fishing, and the source says streams throughout the park and about 35 lakes support non-native fish. The park's staff now use DNA in water samples and genetic samples from fish to learn what lives where. This is the Mount Rainier science brief on the project, as of the source. The park thanks its partners, including the Puyallup Tribe of Indians, USGS, USFWS, the Muckleshoot Tribe of Indians, WDFW, Pierce County and King County.

Aquatic amphibian species of concern: a Cascades frog (top) and Northwestern salamanders eaten by introduced trout (bottom). NPS photos.

A fishless park, filled

The park is the headwaters of several complex cold-water river and lake systems, shaped by seasonal runoff from glaciers and snowmelt. Fish and amphibians are good indicators of an ecosystem's health because they are sensitive to environmental conditions. Historically the lakes were fishless and offered safe breeding pools for amphibians. Brook trout and other non-native fish were introduced to improve fishing. The stocking and spread of non-native fish may be the greatest potential threat to native fish in the park, and it is known to reduce or displace native amphibians of concern and alter ecosystems.

Bull trout, a federally threatened char, live in several drainages of the park. Brook trout, their non-native cousins, can hybridize with, compete with and prey on juvenile bull trout, and are considered a threat to bull trout persistence and recovery in the park. Another char, Dolly Varden, may be present but has not been documented.

Federally threatened bull trout (Salvelinus confluentus). NPS photo.

Two tools

Rare, remote aquatic species make surveys costly and demanding for park staff. The park uses two methods that can better inform recreational and conservation decisions.

Environmental DNA (eDNA). This is genetic material that organisms release into the environment through feces, mucus, skin, scales, hair and carcasses. A pump pulls water through a filter, and after a set amount is filtered, the filter is stored for analysis by lab partners. The park uses eDNA to detect whether fish and amphibians are present or absent in watersheds, mapping which drainages hold which species and which need more intensive sampling.

Collecting an eDNA sample with a vacuum flask and hand pump. NPS photo.

Genetic sampling. Fish are caught by gillnet, hook and line or electrofishing, depending on the species. A clip from the upper tail fin is stored in ethanol until processed. The samples reveal whether a fish was stocked or native, how much it has hybridized, its life history (resident or anadromous) and further detail on species. Appearance alone may not tell a stocked fish from a native one or a hybrid.

Goals and results

The project aims to understand where aquatic species occur using eDNA, to define the population genetic structure and diversity of fish populations to guide future management, and to find out whether Dolly Varden are present. So far, technicians have collected twenty-eight eDNA samples, focusing on the White River, Puyallup, Mowich and Carbon River watersheds because char species may overlap there. They have also collected genetic samples from bull and brook trout, rainbow and cutthroat trout, and coho salmon in lakes and streams.

The Ohanapecosh River, a drainage targeted for eDNA and genetic sampling. NPS/E. Brouwer photo.

Looking ahead to 2022

For the 2022 field season, the park proposed eighty-nine new eDNA sampling sites, in the Huckleberry Creek, Ohanapecosh and Nisqually drainages, aimed at detecting amphibians. It also intends to expand its genetic fish library. Future funding would support analyzing almost 700 char samples collected across the Puyallup watershed by the park and partners including the Puyallup Tribe of Indians and the U.S. Fish and Wildlife Service, to show how char are distributed genetically and how far hybridization extends. Ohanapecosh drainage fish would also be sampled to learn where its rainbow and cutthroat trout came from, so managers can adjust fishing regulations to better protect native species.

Sources

• National Park Service, Mount Rainier National Park, "Fish & Amphibian Inventory: Genetic and Environmental DNA (eDNA) Sampling," Mount Rainier Science Brief, https://www.nps.gov/articles/000/genetic-and-environmental-dna-sampling.htm; rewritten in hubnx's own words.